Background: Today, women constitute about half of medical students in several Western societies, yet women physicians are still underrepresented in surgical specialties and clustered in other branches of medicine. Gender segregation in specialty preference has been found already in medical school. It is important to study the career preferences of our future physicians, as they will influence the maintenance of an adequate supply of physicians in all specialties and the future provision of health care. American and British studies dominate the area of gender and medical careers whereas Swedish studies on medical students’ reasons for specialty preference are scarce. The aim of this study is to investigate and compare Swedish male and female medical students’ specialty preferences and the motives behind them. Methods: Between 2006 and 2009, all last-year medical students at Umea University, Sweden (N = 421), were invited to answer a questionnaire about their future career and family plans. They were asked about their specialty preference and how they rated the impact that the motivational factors had for their choice. The response rate was 89% (N = 372); 58% were women (N = 215) and 42% were men (N = 157). Logistic regression was used to evaluate the independent impact of each motivational factor for specialty preference. Results: On the whole, male and female last-year students opted for similar specialties. Men and women had an almost identical ranking order of the motivational factors. When analyzed separately, male and female students showed both similarities and differences in the motivational factors that were associated with their specialty preference. A majority of the women and a good third of the men intended to work part-time. The motivational factor combining work with family correlated with number of working hours for women, but not for men. Conclusions: The gender similarities in the medical students’ specialty preferences are striking and contrast with research from other Western countries where male and female students show more differences in career aspirations. These similarities should be seized by the health care system in order to counteract the horizontal gender segregation in the physician workforce of today.